Vertebrates rely on innate immune receptors to sense conserved structures from invading microbes. The overall goal of this project is to understand at the molecular level how innate immune receptors recognize flaviviruses, and how this recognition is translated into an immune response. We focus on innate immune recognition of viral genomic RNA in the cytoplasm by the DExD/H-box RNA helicases RIG-I and MDA5. RIGI recognizes short RNA oligonucleotides bearing 5'-triphosphates, while MDA5 recognizes longer, double stranded RNAs. Our first goal is to measure the binding affinities of RIG-I and MDA5 for RNA substrates of various lengths and secondary structures. We will begin to dissect the mechanism of signal transduction of RIG-I and MDA5 by measuring their rates of ATP hydrolysis and their helicase activities in the presence of their preferred RNA substrates. In the major part of our proposal, we will determine the crystal structures of RIG-I and MDA5 in the presence and absence of their preferred RNA ligands. These crystal structures will reveal the conformational changes caused by RNA binding, which will allow us to understand how binding of RNA is translated into an innate immune signal. To test our structure-based model for signal generation, we will engineer mutations designed to alter the signaling and ligand-binding properties of RIG-I and MDA5. Intracellular signaling in response to viral genomic RNA is modulated by another DExD/H-box helicase, LGP2, which interacts directly with RIG-I and MDA5. To understand how LGP2 regulates RIG-I and MDA5 signaling, we will determine the crystal structure of LGP2 in complex with RIG-I or MDA5. Paramyxoviruses inhibit MDA5 signaling by binding MDA5 directly with their V proteins. In order to understand the molecular basis of this viral immune evasion, we will determine the crystal structure of MDA5 in complex with SV5 V. Our structural approach will provide unique mechanistic insights into the generation and regulation of viral RNA sensing by RIG-I and MDA5. In the long term, this work will guide the rational design of novel vaccine adjuvants and immunomodulatory therapeutics targeting RIG-I or MDA5, thus providing new strategies for the prevention and treatment of viral infections.

Public Health Relevance

Our work will provide a detailed understanding at the molecular level of how the innate immune system recognizes genetic material from certain important viral pathogens, including dengue and West Nile viruses, which afftect approximately 100 million people each year and are rapidly spreading. This project will provide some of the necessary tools to create novel therapeutics against these pathogens, such as less toxic vaccine adjuvants, and anti-inflammatory drugs targeting the innate immune response.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Program Projects (P01)
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Special Emphasis Panel (ZRG1-BCMB-K)
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Yale University
New Haven
United States
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Li, Sanshu; Breaker, Ronald R (2017) Identification of 15 candidate structured noncoding RNA motifs in fungi by comparative genomics. BMC Genomics 18:785
Nelson, James W; Atilho, Ruben M; Sherlock, Madeline E et al. (2017) Metabolism of Free Guanidine in Bacteria Is Regulated by a Widespread Riboswitch Class. Mol Cell 65:220-230
Reiss, Caroline W; Strobel, Scott A (2017) Structural basis for ligand binding to the guanidine-II riboswitch. RNA 23:1338-1343
Wang, Jimin; Moore, Peter B (2017) On the interpretation of electron microscopic maps of biological macromolecules. Protein Sci 26:122-129
Wang, Jimin; Askerka, Mikhail; Brudvig, Gary W et al. (2017) Insights into Photosystem II from Isomorphous Difference Fourier Maps of Femtosecond X-ray Diffraction Data and Quantum Mechanics/Molecular Mechanics Structural Models. ACS Energy Lett 2:397-407
Nelson, James W; Breaker, Ronald R (2017) The lost language of the RNA World. Sci Signal 10:
Lomakin, Ivan B; Stolboushkina, Elena A; Vaidya, Anand T et al. (2017) Crystal Structure of the Human Ribosome in Complex with DENR-MCT-1. Cell Rep 20:521-528
Wang, Jimin; Askerka, Mikhail; Brudvig, Gary W et al. (2017) Crystallographic Data Support the Carousel Mechanism of Water Supply to the Oxygen-Evolving Complex of Photosystem II. ACS Energy Lett 2:2299-2306
Greenlee, Etienne B; Stav, Shira; Atilho, Ruben M et al. (2017) Challenges of Ligand Identification for the Second Wave of Orphan Riboswitch Candidates. RNA Biol :0
Arachchilage, Gayan Mirihana; Sherlock, Madeline E; Weinberg, Zasha et al. (2017) SAM-VI RNAs Selectively Bind S-adenosylmethionine and Exhibit Similarities to SAM-III Riboswitches. RNA Biol :0

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